Built with R version 3.6.3

0.1 Setup

0.1.1 Environment

##          used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 487947 26.1    1073392 57.4         NA   641482 34.3
## Vcells 926847  7.1    8388608 64.0      32768  1768755 13.5
## Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
## logical.return = TRUE, : there is no package called 'Bitr'
## Warning: package 'Bitr' is not available (for R version 3.6.3)
## Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
## logical.return = TRUE, : there is no package called 'Bitr'

0.2 QC and Data filtering

0.2.1 QC & Normalisation

##  [1] "mt-Nd1"  "mt-Nd2"  "mt-Co1"  "mt-Co2"  "mt-Atp8" "mt-Atp6" "mt-Co3" 
##  [8] "mt-Nd3"  "mt-Nd4l" "mt-Nd4"  "mt-Nd5"  "mt-Nd6"  "mt-Cytb"

## pdf 
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## 'data.frame':    1907 obs. of  4 variables:
##  $ orig.ident  : Factor w/ 1 level "SeuratProject": 1 1 1 1 1 1 1 1 1 1 ...
##  $ nCount_RNA  : num  9729 8060 634 7692 2296 ...
##  $ nFeature_RNA: int  2510 2117 411 2230 1045 2140 2589 1564 2767 1849 ...
##  $ percent.mito: num  0.0363 0.0362 0.0994 0.0261 0.2134 ...
## An object of class Seurat 
## 13172 features across 1526 samples within 1 assay 
## Active assay: RNA (13172 features, 0 variable features)

## pdf 
##   3
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## An object of class Seurat 
## 13172 features across 1907 samples within 1 assay 
## Active assay: RNA (13172 features, 0 variable features)
## An object of class Seurat 
## 13172 features across 1526 samples within 1 assay 
## Active assay: RNA (13172 features, 0 variable features)

0.2.2 Dimension reduction

## pdf 
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##                 2

## pdf 
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##                 2
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 1526
## Number of edges: 55479
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.9179
## Number of communities: 3
## Elapsed time: 0 seconds

## pdf 
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##                 2

## pdf 
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##                 2

0.2.4 Subset data by ADT_Cd226 expression

## An object of class Seurat 
## 13173 features across 1526 samples within 2 assays 
## Active assay: RNA (13172 features, 2000 variable features)
##  1 other assay present: ADT
##  3 dimensional reductions calculated: pca, tsne, umap
##       25%       75% 
## 0.3774276 1.2486700
## [1] 384
## [1] 756
## [1] 386
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##  [225] Neg  Dim  High High Neg  High Dim  High Dim  High Dim  Neg  High Dim 
##  [239] High Dim  Neg  Neg  Dim  Dim  Dim  Dim  High Dim  Dim  Dim  High Dim 
##  [253] Dim  High Dim  Dim  Neg  Neg  Neg  Dim  High Neg  Dim  Dim  Dim  Dim 
##  [267] Neg  High Neg  High Dim  Neg  Neg  High Neg  Neg  Dim  High High Neg 
##  [281] Neg  Dim  High Neg  High Dim  High High Dim  Dim  Dim  High High Dim 
##  [295] Dim  High Dim  High High Dim  Neg  Dim  Dim  Dim  High Dim  Neg  Neg 
##  [309] Neg  High High Dim  Neg  Neg  Dim  Dim  Dim  High Dim  Dim  Dim  Dim 
##  [323] Neg  Neg  Dim  Dim  High Dim  Neg  Dim  High Neg  Dim  High High High
##  [337] High Dim  Dim  Neg  Dim  High Dim  Dim  High High Dim  Neg  Dim  Dim 
##  [351] Dim  Dim  Dim  Dim  Dim  Dim  Dim  Dim  High Neg  High Neg  Dim  Dim 
##  [365] Neg  Neg  Dim  Dim  Dim  Dim  Dim  Neg  Dim  High Dim  Dim  Dim  Dim 
##  [379] Dim  Neg  High Dim  Dim  Dim  High Dim  High Neg  Neg  Dim  Neg  Dim 
##  [393] Dim  High Dim  Neg  Neg  Dim  High Neg  Neg  Neg  Neg  Dim  Dim  Neg 
##  [407] Neg  High Dim  Dim  Dim  Dim  Neg  Neg  Dim  High Dim  High High High
##  [421] Dim  High Dim  Dim  Dim  Neg  Dim  High Dim  Neg  High Dim  Dim  Dim 
##  [435] Neg  Dim  Dim  Dim  Dim  High Dim  High High Neg  High Dim  High Neg 
##  [449] Dim  Dim  Neg  Dim  Neg  Dim  Dim  Dim  High Neg  High High Dim  Neg 
##  [463] High High Dim  Neg  Dim  Dim  Neg  Dim  Neg  Dim  Neg  High Dim  Neg 
##  [477] Dim  Dim  Dim  Dim  Dim  Dim  Dim  Dim  High High Neg  High Dim  Dim 
##  [491] Dim  Dim  Neg  Neg  High Dim  High Neg  Dim  Dim  Dim  Neg  High High
##  [505] Dim  Dim  High Dim  Neg  Neg  High Dim  Dim  High High Dim  Dim  Dim 
##  [519] Dim  Dim  High Neg  Dim  Neg  Neg  Dim  Neg  Dim  Dim  High Neg  Neg 
##  [533] Dim  Dim  Dim  Dim  High Dim  Neg  High Dim  Dim  High High Dim  Dim 
##  [547] High High Dim  Dim  Dim  High Dim  Dim  Dim  High Dim  High Dim  High
##  [561] Neg  Dim  Neg  Dim  Dim  Dim  Dim  High High Dim  Dim  Dim  High High
##  [575] Neg  High Neg  Dim  Neg  Dim  High High Dim  Neg  Dim  Dim  High High
##  [589] Neg  Neg  Dim  Dim  Dim  Neg  Dim  Dim  Dim  Dim  Neg  Neg  Neg  Neg 
##  [603] Dim  Dim  Dim  High Dim  Neg  Dim  Dim  High Neg  Dim  High Neg  Neg 
##  [617] Neg  Neg  Neg  High High High Dim  Neg  Neg  Dim  Dim  Dim  Dim  Dim 
##  [631] Dim  Dim  Neg  Dim  Dim  Dim  Dim  Dim  Dim  Neg  Neg  Neg  Dim  Dim 
##  [645] Neg  High High Dim  Neg  Neg  Dim  Neg  High Neg  Dim  Dim  Dim  High
##  [659] Dim  Neg  Dim  Dim  Dim  Dim  Dim  Dim  High Dim  High Dim  Neg  High
##  [673] Neg  Dim  Dim  Dim  Neg  High Neg  High Neg  Neg  Dim  Neg  Dim  Dim 
##  [687] Dim  Dim  Dim  High High High Dim  High Dim  High Dim  Neg  High Dim 
##  [701] Dim  Dim  Neg  Dim  Dim  High Neg  Dim  Dim  High Neg  High Neg  Dim 
##  [715] Dim  Dim  Dim  Dim  Dim  Dim  High Dim  Dim  Dim  High Dim  High Neg 
##  [729] Dim  High Dim  Neg  Neg  Dim  Dim  Neg  Dim  High Dim  Neg  Dim  Dim 
##  [743] Neg  Dim  High Dim  High Neg  Dim  High Dim  Dim  Dim  Neg  Dim  Dim 
##  [757] Neg  High Dim  Dim  Dim  Neg  Dim  High Dim  Dim  Neg  Neg  Dim  Neg 
##  [771] High Dim  Dim  Dim  High High Dim  Dim  Dim  Neg  High Dim  Neg  Neg 
##  [785] Dim  Dim  Dim  Neg  Dim  High Dim  High Dim  High High Dim  High Dim 
##  [799] Neg  Neg  Dim  Dim  Dim  Neg  Neg  Neg  Neg  High Dim  Neg  Dim  High
##  [813] Dim  Neg  Neg  Dim  Neg  Dim  Dim  Dim  High Neg  High Dim  Dim  Neg 
##  [827] High Neg  Neg  Dim  High Neg  High Dim  Neg  Dim  High High Neg  Dim 
##  [841] Dim  Dim  Dim  Dim  Dim  Dim  Dim  Neg  Dim  Neg  Dim  High Neg  Neg 
##  [855] Dim  Dim  High Neg  High High Dim  Dim  Dim  Neg  Neg  Neg  Dim  High
##  [869] High Dim  Dim  Dim  Dim  Dim  Dim  Dim  High High Dim  High Neg  Neg 
##  [883] High Neg  Dim  Neg  Dim  High High High Neg  High Dim  Dim  High Dim 
##  [897] Dim  Dim  Neg  High High Dim  Dim  Dim  Dim  Neg  High Neg  High Dim 
##  [911] Dim  High Dim  High Dim  Neg  Dim  Dim  High High High High High High
##  [925] High High High High Dim  Dim  Dim  Dim  Dim  Neg  Dim  Neg  Dim  High
##  [939] Dim  Dim  Dim  Neg  Neg  Dim  Dim  Dim  High Dim  High Neg  High Dim 
##  [953] High Neg  High Dim  Neg  Dim  Dim  Dim  Dim  High Dim  Neg  Neg  Dim 
##  [967] Dim  Dim  High Dim  Dim  High High Dim  Neg  Neg  Dim  High Dim  Dim 
##  [981] High Neg  High High Dim  Neg  Dim  High Neg  Neg  Neg  High High Dim 
##  [995] High Dim  High Dim  Neg  Dim  High Neg  Neg  Dim  Dim  High Neg  High
## [1009] High Dim  Neg  High Dim  Neg  Dim  Dim  Dim  Neg  Dim  Dim  Dim  Dim 
## [1023] Dim  High Dim  Dim  High Neg  High Neg  Neg  Neg  Dim  High High Neg 
## [1037] High Dim  Dim  Neg  Dim  Dim  Dim  High Dim  High Dim  Neg  Dim  Dim 
## [1051] High Dim  High Dim  Neg  High High Dim  Dim  Neg  Neg  Neg  Dim  High
## [1065] Dim  High Dim  Dim  Dim  High Dim  Neg  High Neg  Dim  Dim  Dim  High
## [1079] Dim  Neg  Neg  Neg  High Neg  High High High Dim  Dim  Neg  Dim  Neg 
## [1093] High Neg  Dim  Dim  Dim  Neg  Neg  Neg  Neg  High Dim  Dim  Dim  High
## [1107] Neg  Dim  Neg  Dim  Dim  High Neg  Dim  High Neg  High Neg  Dim  Dim 
## [1121] Dim  Neg  High Dim  Dim  Dim  High Dim  Dim  Dim  High Neg  Dim  Dim 
## [1135] Dim  Neg  Dim  Dim  Neg  High Dim  High Neg  Dim  Dim  Neg  High Dim 
## [1149] High Neg  Neg  Neg  High Neg  Dim  Dim  Dim  Dim  Dim  Neg  Neg  High
## [1163] High High High Dim  High Dim  Neg  Dim  Neg  Neg  Dim  High Dim  Neg 
## [1177] High Dim  High Dim  High High Dim  High High High Neg  Neg  High High
## [1191] Dim  Dim  Dim  Neg  Dim  Dim  Dim  Dim  Dim  Neg  High Neg  Dim  Dim 
## [1205] High High Dim  Neg  Dim  Dim  Dim  Dim  High High Neg  Dim  Dim  Dim 
## [1219] High High Dim  Dim  Dim  High High High Dim  Dim  Dim  High Neg  Dim 
## [1233] Neg  Dim  Dim  High High Dim  Dim  Dim  Neg  Dim  Dim  Dim  High Neg 
## [1247] Dim  Dim  Dim  Neg  High Dim  Dim  High High Dim  Dim  Neg  Dim  Neg 
## [1261] Neg  High Dim  Neg  Neg  Dim  Dim  Dim  High High Neg  High High Dim 
## [1275] High Neg  Dim  Dim  High Dim  High Dim  High Dim  Dim  Dim  High High
## [1289] Dim  Dim  Dim  Dim  Dim  High Dim  Neg  High Dim  Dim  Neg  Dim  Dim 
## [1303] Dim  High Dim  High Neg  High High Dim  Neg  Neg  Dim  Neg  Neg  Neg 
## [1317] Neg  Dim  Dim  Dim  Dim  High Dim  High Dim  High Dim  Dim  Dim  Dim 
## [1331] High Dim  Dim  Neg  Dim  Dim  High Dim  Dim  Dim  High Dim  Dim  Dim 
## [1345] Neg  Neg  Dim  High Neg  Dim  Neg  High High High Dim  Neg  Dim  Dim 
## [1359] Neg  Dim  Dim  Dim  Neg  Dim  Neg  Dim  Neg  Dim  High Dim  Dim  Dim 
## [1373] Neg  Dim  High High High Neg  Dim  Neg  Dim  High Neg  Dim  Dim  Neg 
## [1387] Neg  Neg  Dim  Dim  Dim  High Dim  Dim  Neg  Dim  Dim  Neg  Dim  Dim 
## [1401] High Dim  Neg  Dim  Dim  Neg  Dim  Dim  Neg  Dim  Dim  Neg  Dim  Dim 
## [1415] Dim  Neg  High Dim  High High Dim  Dim  Dim  Neg  Dim  High Neg  High
## [1429] Dim  High High Dim  Dim  Dim  Dim  Neg  High Neg  High Dim  Dim  Neg 
## [1443] Neg  Dim  Neg  Neg  Neg  High Neg  Dim  Dim  Dim  High Dim  Dim  High
## [1457] High Dim  Dim  Dim  Neg  High Neg  High Neg  High Neg  Neg  Dim  Dim 
## [1471] High Dim  Dim  Dim  Dim  Neg  Neg  Neg  Dim  Neg  Dim  High Dim  Dim 
## [1485] Neg  Neg  Neg  Dim  Neg  Dim  Dim  Dim  Dim  Dim  Neg  Neg  Dim  Dim 
## [1499] Neg  Neg  Dim  Neg  High Neg  High Dim  High High Neg  Dim  High Dim 
## [1513] Neg  Neg  Neg  Dim  Dim  Neg  High Dim  Dim  High High High Neg  Dim 
## Levels: Dim High Neg
## AAACCCAGTAATCAAG AAACCCAGTCTGTCCT AAACGCTAGTCACGCC AAAGAACGTTAACAGA 
##              Neg              Dim             High             High 
## AAAGGATAGTCCTACA AAAGGATGTATCGTAC 
##              Neg              Neg 
## Levels: Dim High Neg
## [1] "Dim"  "High" "Neg"
## [1] "Neg"  "Dim"  "High"
## NULL
## [1] "Neg"  "Dim"  "High"

0.2.5 ADT cluster # and %

## 
##  Neg  Dim High 
##  384  756  386
## 
##      Neg      Dim     High 
## 25.16383 49.54128 25.29489

0.2.6 Visualising ADT subsets

## pdf 
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0.3 Differential gene expression

0.4 Visualisation

0.4.1 Volcano DEGs

## [1] "High" "Neg"  "NS"
##  [1] "Cd226"   "Eomes"   "Rora"    "Ifng"    "Cd69"    "Gzma"    "Gzmb"   
##  [8] "Cd48"    "Gzmk"    "Icam1"   "Crtam"   "Lag3"    "Tnfrsf9" "Cd247"

## pdf 
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0.5 GSEA

0.5.1 Convert Symbol to EntrezID

##  [1] "ACCNUM"       "ALIAS"        "ENSEMBL"      "ENSEMBLPROT"  "ENSEMBLTRANS"
##  [6] "ENTREZID"     "ENZYME"       "EVIDENCE"     "EVIDENCEALL"  "GENENAME"    
## [11] "GO"           "GOALL"        "IPI"          "MGI"          "ONTOLOGY"    
## [16] "ONTOLOGYALL"  "PATH"         "PFAM"         "PMID"         "PROSITE"     
## [21] "REFSEQ"       "SYMBOL"       "UNIGENE"      "UNIPROT"
## [1] 12127     7

0.5.2 msigDB

## [1] 869   7
## [1] 753   7
##                                                                                                            ID
## GO_T_CELL_ACTIVATION                                                                     GO_T_CELL_ACTIVATION
## GO_LEUKOCYTE_CELL_CELL_ADHESION                                               GO_LEUKOCYTE_CELL_CELL_ADHESION
## GO_LYMPHOCYTE_DIFFERENTIATION                                                   GO_LYMPHOCYTE_DIFFERENTIATION
## GO_T_CELL_DIFFERENTIATION                                                           GO_T_CELL_DIFFERENTIATION
## GO_REGULATION_OF_T_CELL_ACTIVATION                                         GO_REGULATION_OF_T_CELL_ACTIVATION
## GO_POSITIVE_REGULATION_OF_LEUKOCYTE_CELL_CELL_ADHESION GO_POSITIVE_REGULATION_OF_LEUKOCYTE_CELL_CELL_ADHESION
##                                                                                                   Description
## GO_T_CELL_ACTIVATION                                                                     GO_T_CELL_ACTIVATION
## GO_LEUKOCYTE_CELL_CELL_ADHESION                                               GO_LEUKOCYTE_CELL_CELL_ADHESION
## GO_LYMPHOCYTE_DIFFERENTIATION                                                   GO_LYMPHOCYTE_DIFFERENTIATION
## GO_T_CELL_DIFFERENTIATION                                                           GO_T_CELL_DIFFERENTIATION
## GO_REGULATION_OF_T_CELL_ACTIVATION                                         GO_REGULATION_OF_T_CELL_ACTIVATION
## GO_POSITIVE_REGULATION_OF_LEUKOCYTE_CELL_CELL_ADHESION GO_POSITIVE_REGULATION_OF_LEUKOCYTE_CELL_CELL_ADHESION
##                                                        GeneRatio   BgRatio
## GO_T_CELL_ACTIVATION                                      82/685 448/16881
## GO_LEUKOCYTE_CELL_CELL_ADHESION                           61/685 334/16881
## GO_LYMPHOCYTE_DIFFERENTIATION                             60/685 340/16881
## GO_T_CELL_DIFFERENTIATION                                 48/685 242/16881
## GO_REGULATION_OF_T_CELL_ACTIVATION                        52/685 315/16881
## GO_POSITIVE_REGULATION_OF_LEUKOCYTE_CELL_CELL_ADHESION    42/685 211/16881
##                                                              pvalue
## GO_T_CELL_ACTIVATION                                   1.854225e-31
## GO_LEUKOCYTE_CELL_CELL_ADHESION                        1.677063e-23
## GO_LYMPHOCYTE_DIFFERENTIATION                          2.466146e-22
## GO_T_CELL_DIFFERENTIATION                              2.865564e-20
## GO_REGULATION_OF_T_CELL_ACTIVATION                     3.564098e-18
## GO_POSITIVE_REGULATION_OF_LEUKOCYTE_CELL_CELL_ADHESION 6.108670e-18
##                                                            p.adjust
## GO_T_CELL_ACTIVATION                                   9.211790e-28
## GO_LEUKOCYTE_CELL_CELL_ADHESION                        4.165824e-20
## GO_LYMPHOCYTE_DIFFERENTIATION                          4.083938e-19
## GO_T_CELL_DIFFERENTIATION                              3.559030e-17
## GO_REGULATION_OF_T_CELL_ACTIVATION                     3.541288e-15
## GO_POSITIVE_REGULATION_OF_LEUKOCYTE_CELL_CELL_ADHESION 4.650126e-15
##                                                              qvalue
## GO_T_CELL_ACTIVATION                                   7.539865e-28
## GO_LEUKOCYTE_CELL_CELL_ADHESION                        3.409733e-20
## GO_LYMPHOCYTE_DIFFERENTIATION                          3.342709e-19
## GO_T_CELL_DIFFERENTIATION                              2.913072e-17
## GO_REGULATION_OF_T_CELL_ACTIVATION                     2.898550e-15
## GO_POSITIVE_REGULATION_OF_LEUKOCYTE_CELL_CELL_ADHESION 3.806136e-15
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          geneID
## GO_T_CELL_ACTIVATION                                   Adam8/Anxa1/Apbb1ip/B2m/Bcl3/Camk4/Card11/Casp8/Ccl5/Ccnd3/Ccr2/Cd274/Cd44/Cd47/Cd80/Cd86/Cd8b1/Cdc42/Chd7/Coro1a/Ctla4/Dock2/Dock8/Egr1/Flot2/Gata3/Gpr18/Gpr183/Grap2/Gsn/H2-M3/Havcr2/Icam1/Icos/Ifng/Il18r1/Il2ra/Il7r/Irf1/Irf4/Itgal/Itk/Klrk1/Lck/Lcp1/Lfng/Lgals1/Lgals3/Lgals9/Lilr4b/Map3k8/March7/Msn/Nfkbid/Nfkbiz/Nlrc3/Pag1/Pik3cd/Ppp3ca/Ppp3cb/Prr7/Psmb10/Ptger4/Pycard/Rac2/Rasal3/Rasgrp1/Rhoa/Ripk2/Rora/Runx2/Runx3/Satb1/Sema4a/Smad7/Socs1/Spn/Thy1/Tnfaip8l2/Vsir/Zc3h12a/Zfp683
## GO_LEUKOCYTE_CELL_CELL_ADHESION                                                                                                                                                    Adam8/Anxa1/Card11/Ccl5/Ccr2/Cd274/Cd44/Cd47/Cd80/Cd86/Cdc42/Coro1a/Ctla4/Cx3cr1/Dock8/Ezr/Flot2/Gata3/Grap2/H2-M3/Havcr2/Icam1/Icos/Ifng/Il2ra/Il7r/Irf1/Itgal/Itgb1/Itgb2/Itgb7/Klrk1/Lck/Lgals1/Lgals3/Lgals9/Lilr4b/Map3k8/March7/Msn/Nfkbid/Nfkbiz/Pag1/Pycard/Rac2/Rasal3/Rasgrp1/Rhoa/Ripk2/Runx3/Selplg/Skap1/Smad7/Socs1/Spn/Stk10/Thy1/Tnfaip8l2/Vsir/Wnk1/Zc3h12a
## GO_LYMPHOCYTE_DIFFERENTIATION                                                                                                                                                             Adam8/Anxa1/B2m/Bcl3/Camk4/Card11/Ccr2/Cd80/Cd86/Chd7/Ctla4/Dock10/Dock2/Egr1/Flt3l/Gata3/Gpr18/Gpr183/H2-M3/Id2/Ifng/Il18r1/Il2ra/Il7r/Inpp5d/Irf1/Irf2bp2/Irf4/Itgb1/Itk/Klf6/Lck/Lfng/Lgals1/Lgals9/Lilr4b/Nfkbid/Nfkbiz/Notch2/Pglyrp2/Pik3cd/Plcl2/Ppp3cb/Prr7/Ptger4/Ptk2b/Rasgrp1/Rhoa/Ripk2/Rora/Runx2/Runx3/Satb1/Sema4a/Smad7/Socs1/Spn/Vsir/Zc3h12a/Zfp683
## GO_T_CELL_DIFFERENTIATION                                                                                                                                                                                                                                              Adam8/Anxa1/B2m/Bcl3/Camk4/Card11/Ccr2/Cd80/Cd86/Chd7/Ctla4/Dock2/Egr1/Gata3/Gpr18/Gpr183/H2-M3/Ifng/Il18r1/Il2ra/Il7r/Irf1/Irf4/Itk/Lck/Lfng/Lgals9/Lilr4b/Nfkbid/Nfkbiz/Pik3cd/Ppp3cb/Prr7/Ptger4/Rasgrp1/Rhoa/Ripk2/Rora/Runx2/Runx3/Satb1/Sema4a/Smad7/Socs1/Spn/Vsir/Zc3h12a/Zfp683
## GO_REGULATION_OF_T_CELL_ACTIVATION                                                                                                                                                                                                     Adam8/Anxa1/Camk4/Card11/Ccl5/Ccr2/Cd274/Cd47/Cd80/Cd86/Cdc42/Coro1a/Ctla4/Dock8/Flot2/Gata3/Grap2/Gsn/H2-M3/Havcr2/Icos/Ifng/Il2ra/Il7r/Irf1/Irf4/Klrk1/Lck/Lgals1/Lgals3/Lgals9/Lilr4b/Map3k8/March7/Nfkbid/Nfkbiz/Pag1/Pycard/Rac2/Rasal3/Rasgrp1/Rhoa/Ripk2/Runx3/Smad7/Socs1/Spn/Thy1/Tnfaip8l2/Vsir/Zc3h12a/Zfp683
## GO_POSITIVE_REGULATION_OF_LEUKOCYTE_CELL_CELL_ADHESION                                                                                                                                                                                                                                               Adam8/Anxa1/Card11/Ccl5/Ccr2/Cd274/Cd44/Cd47/Cd80/Cd86/Cdc42/Coro1a/Ctla4/Dock8/Flot2/Gata3/Grap2/H2-M3/Havcr2/Icam1/Icos/Ifng/Il2ra/Il7r/Klrk1/Lck/Lgals1/Lgals9/Lilr4b/Map3k8/Nfkbid/Nfkbiz/Pycard/Rasal3/Rasgrp1/Rhoa/Ripk2/Runx3/Skap1/Socs1/Thy1/Vsir
##                                                        Count
## GO_T_CELL_ACTIVATION                                      82
## GO_LEUKOCYTE_CELL_CELL_ADHESION                           61
## GO_LYMPHOCYTE_DIFFERENTIATION                             60
## GO_T_CELL_DIFFERENTIATION                                 48
## GO_REGULATION_OF_T_CELL_ACTIVATION                        52
## GO_POSITIVE_REGULATION_OF_LEUKOCYTE_CELL_CELL_ADHESION    42

## pdf 
##   3
## quartz_off_screen 
##                 2